When Pandoc converts Markdown to LaTeX, it uses a template that speciefies what header and footer material to add (http://pandoc.org/README.html#templates http:

When Pandoc converts Markdown to LaTeX, it uses a template that speciefies what header and footer material to add (http://pandoc.org/README.html#templates http://pandoc.org/README.html#templates). You could modify the default template to use whatever style file you want. Pandoc also supports references with a .bib file, and inserting TeX math formulae between dollar signs.